You might consider parent and child post types (see http://justintadlock.com/archives/2013/10/07/post-relationships-parent-to-child for a bit about this). You can see examples of this kind of thing in the Sensei learning management plugin, which has a Course post type with other post types as children: lessons, quizzes, etc. You’ll probably want to explore different possibilities.
I would not worry too much about the URL structure–just don’t alter it to the point that WordPress gets confused. If you make major changes to the site you will end up needing to create 301 redirects anyway, and you can use regular expressions to make your life easier there.
